[R] (lme4: lmer) mcmcsamp: Error in if (var(y) == 0)

From: David Reitter <dreitter_at_inf.ed.ac.uk>
Date: Thu, 24 Jan 2008 08:40:15 +0000


I've got a problem with "mcmcsamp" used with glmer objects produced with "lmer" from the lme4 package.

When calling mcmcsamp, I get the error

Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed

This does not occur with all models, but I can't find anything wrong with the dataset.

If the error is in my data, can someone tell me what I am looking for? (Can I print the source code of the mcmcsamp method for glmer objects? I'd like to know what "y" stands for.)

Many thanks for your advice!

===

> sessionInfo()

R version 2.6.1 (2007-11-26)
i686-pc-linux-gnu

locale:
LC_CTYPE
=
en_GB
.UTF
-8
;LC_NUMERIC
=
C
;LC_TIME
=
en_GB
.UTF
-8
;LC_COLLATE
=
en_GB
.UTF
-8
;LC_MONETARY
=
en_GB
.UTF
-8
;LC_MESSAGES
=
en_GB
.UTF
-8
;LC_PAPER
=
en_GB
.UTF
-8
;LC_NAME
=
C
;LC_ADDRESS
=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] languageR_0.4 coda_0.13-1 lme4_0.99875-9 Matrix_0.999375-4
[5] zipfR_0.6-0 lattice_0.17-2

loaded via a namespace (and not attached): [1] grid_2.6.1 rcompgen_0.1-17

> emnlp.m1 <- lmer(primed ~ (role * derivation)/(log(dist.time) *
log(rule.freq)) + (1 + log(dist.time) | target.utt), family=binomial, data=data.utts )
> summary(emnlp.m1)

Error: cannot allocate vector of size 120.3 Mb
> emnlp.m1

Generalized linear mixed model fit using Laplace Formula: primed ~ (role * derivation)/(log(dist.time) * log(rule.freq)) + (1 + log(dist.time) | target.utt)

    Data: data.utts
  Family: binomial(logit link)

      AIC BIC logLik deviance
  1145907 1146131 -572935 1145869
...

                                                 Pr(>|z|)
...
rolei:derivationI:log(dist.time)                 < 2e-16 ***
roler:derivationI:log(dist.time)                 < 2e-16 ***
rolei:derivationN:log(dist.time)                 < 2e-16 ***
roler:derivationN:log(dist.time)                0.000187 ***
...
> class(emnlp.m1)

[1] "glmer"
attr(,"package")
[1] "lme4"
> mc <- mcmcsamp(emnlp.m1)
> summary(mc)
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
...
2. Quantiles for each variable:
                                                     Mean SD Naive SE
(
rolei:derivationI:log(dist.time)                -2.19615 NA       NA
roler:derivationI:log(dist.time)                -1.36876 NA       NA
...
                                                     2.5%       
25%      50%
rolei:derivationI:log(dist.time)                -2.19615 -2.19615  
-2.19615
roler:derivationI:log(dist.time)                -1.36876 -1.36876  
-1.36876

> traceback()

11: asMethod(object)
10: as(object, superClass)

9: validityMethod(as(object, superClass))
8: identical(x, TRUE)
7: anyStrings(validityMethod(as(object, superClass)))
6: validObject(.Object)
5: initialize(value, ...)
4: initialize(value, ...)
3: new(if (is(object, "glmer")) "summary.glmer" else {
        if (is(object, "lmer"))
            "summary.lmer"
        else "summary.mer"

    }, object, isG = glz, methTitle = methTitle, logLik = llik, ngrps = sapply(object_at_flist,
        function(x) length(levels(x))), sigma = .Call(mer_sigma,
        object, REML), coefs = coefs, vcov = vcov, REmat = REmat,
        AICtab = AICframe)

2: summary(emnlp.m1)
1: summary(emnlp.m1)
--
David Reitter
ICCS/HCRC, Informatics, University of Edinburgh
http://www.david-reitter.com

______________________________________________
R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Received on Thu 24 Jan 2008 - 08:45:53 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 24 Jan 2008 - 09:30:08 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive